Variant report

Variant	rs12654351
Chromosome Location	chr5:56988506-56988507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:56978767..56981076-chr5:56987149..56990064,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10057804	1.00[ASN][1000 genomes]
rs10077188	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs10487615	1.00[ASN][1000 genomes]
rs12153068	1.00[EUR][1000 genomes]
rs12189365	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652479	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12654040	1.00[ASN][1000 genomes]
rs12654850	0.83[EUR][1000 genomes]
rs12654963	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12655658	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12658940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16887298	1.00[ASN][1000 genomes]
rs2215419	0.98[ASN][1000 genomes]
rs4700209	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58041565	0.91[ASN][1000 genomes]
rs58245968	0.95[EUR][1000 genomes]
rs58266257	1.00[ASN][1000 genomes]
rs59516621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59697426	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60219417	0.89[EUR][1000 genomes]
rs61220614	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6862527	0.91[ASN][1000 genomes]
rs6876911	0.89[EUR][1000 genomes]
rs6883451	0.95[EUR][1000 genomes]
rs6883485	0.95[EUR][1000 genomes]
rs73085594	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089817	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089845	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73089868	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089872	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089877	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73089897	0.83[EUR][1000 genomes]
rs7702309	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7713500	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap]
rs7714714	1.00[ASN][1000 genomes]
rs7717808	1.00[ASN][1000 genomes]
rs7729312	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7731160	1.00[CEU][hapmap]
rs7734079	1.00[ASN][1000 genomes]
rs7734787	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56984200-56988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:56985600-56990400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:56986600-56989800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:56986800-56988600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:56986800-56991800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:56987000-56992800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:56987200-56988600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr5:56987200-56989200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:56987200-56989800	Enhancers	K562	blood
10	chr5:56987400-56988600	Weak transcription	Esophagus	oesophagus
11	chr5:56987400-56988600	Weak transcription	Fetal Heart	heart
12	chr5:56987400-56988800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:56987400-56988800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:56987400-56994800	Weak transcription	Right Ventricle	heart
15	chr5:56987600-56988600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:56987600-56988600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:56987600-56988600	Weak transcription	Brain Substantia Nigra	brain
18	chr5:56987600-56988800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:56987600-56989000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:56987600-56989000	Weak transcription	Spleen	Spleen
21	chr5:56987600-56989200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:56987600-56991400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:56987600-56991800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:56988000-56988600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:56988200-56988600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:56988200-56989200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:56988200-56989200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:56988200-56989200	Enhancers	Left Ventricle	heart
29	chr5:56988200-56989600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr5:56988200-56989600	Enhancers	Ovary	ovary
31	chr5:56988200-56990000	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:56988200-56993400	Enhancers	Brain Angular Gyrus	brain
33	chr5:56988400-56988600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:56988400-56988600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:56988400-56988600	Enhancers	Brain Hippocampus Middle	brain
36	chr5:56988400-56989000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:56988400-56989000	Enhancers	Aorta	Aorta
38	chr5:56988400-56989200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:56988400-56989200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:56988400-56989200	Enhancers	Pancreas	Pancrea
41	chr5:56988400-56989200	Enhancers	Right Atrium	heart
42	chr5:56988400-56989200	Enhancers	HMEC	breast
43	chr5:56988400-56989200	Enhancers	HSMM	muscle
44	chr5:56988400-56989200	Enhancers	NHEK	skin
45	chr5:56988400-56989200	Enhancers	Osteobl	bone
46	chr5:56988400-56989400	Enhancers	Liver	Liver
47	chr5:56988400-56989400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr5:56988400-56989600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:56988400-56989600	Enhancers	Psoas Muscle	Psoas
50	chr5:56988400-56989600	Enhancers	Skeletal Muscle Female	skeletal muscle

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